[WIP] Main table JavaFX migration

[tobiasdiez]

This PR tracks the progress of the migration of the maintable to JavaFX. See also the Maintable in JavaFX project. The current version can be downloaded here.

Please report any bugs that appear or missing features, which are not listed below. Moreover, we appreciate feedback about the general design (what do guys like, what not)

Known bugs:

• Some input controls (like check boxes) look odd
• Smaller things outlined here and here
• Drag & drop to and from the table does not work Implement drag and drop for maintable #3765
• Ranking is not shown (and thus not editable)
• Float mode does not work (partly because of unresolved feature request for Java) code to fix
• Linux / Mac OS: Resizing the columns per drag & drop does not work nicely ([WIP] Main table JavaFX migration #3621 (comment))
• Linux: Column separator are not shown on hover ([WIP] Main table JavaFX migration #3621 (comment))
• Performance of search is poor for large databases Search results not updated after import #1513 (comment)
• Magnifier icon is not colored correctly - we accept that workaround until we implement something really cool as proposed at Magnifier does not change its colors any more #3535 Follow up at Implement ChipView for the search koppor/jabref#341
• Mouse wheel for tabs in entry editor works in the wrong way - up/down reversed in comparison to Firefox (by @koppor) Follow up at Mouse wheel down should scroll right (and not left) #4089
• When in the maintable, Ctrl+F does not focus the search field (by @koppor) Follow up at Ctrl+F does not select the search field #3062
• Import does not work, see [WIP] Main table JavaFX migration #3621 (comment)
• Trailing thread even after JabRef is closed [WIP] Main table JavaFX migration #3621 (comment)
• The colors have to harmonized and sometimes the text is hard to read (black on dark background e.g. in the search or for active rows). Reported in Improve UX of main toolbar #3678 (comment).
• Deleting of entries does not work, leads to exception
• When columns are reorded by drag & drop, then the new order is not saved (i.e. lost after closing JabRef)
• Reordering of tabs using drag'n'drop is not possible any more (by @koppor): code to fix or wait until Java 10
• Columns cannot be resized even if there is an <-> arrow indicated that it would be possible (by @koppor)
• The size of the entry editor sometimes resets leading to a very small editor
• The columns are slightly sized too large if a vertical scrollbar is visible
• The icons in the right toolbar of the entry editor are sized to small
• Saving a file leads to an IllegalStateException
• The searchbar sometimes steals the focus from the maintable.
• JabRef might no longer start on MacOS Entry right-click and table display #3267 (comment)
• JabRef might freeze on Linux New entry not selected in entry table when entering data in field used for sorting #3373 (comment)
• CTRL + TAB does only sometimes work. The toolbar steals the focus. Might be fixed by Make JavaFX a first-class citizen #3684
• Changes to entries don't mark database as changed.
• File annotation tab is not shown and throws exception [WIP] Main table JavaFX migration #3621 (comment)
• Paste of new entries does not work
• It is no longer possible to select multiple entries by holding mouse button: code to fix

Changelog:

Fixed:

• Italic text is now rendered correctly. LaTeX \textit{..} is not redered correctly in Main table #3356
• The entry editor no longer gets corrupted after using the source tab. Selecting new entry causes editing panel to become corrupted and not accept input #3532 Entry preview and editor blank after  #3608 Editor gets stuck and refuses to show the fields #3616
• We fixed multiple issues where entries did not show up after import if a search was active. Search results not updated after import #1513 New entries should be shown when matching the current selection (search, web search) #3219
• We fixed an issue where the group tree was not updated correctly after an entry was changed. Re-evaluate table after pasting entry or editing an antry #3618
• We fixed an issue where a right-click in the main table selected a wrong entry. Entry right-click and table display #3267
• We fixed an issue where in rare cases entries where overlayed in the main table. Entry Table occasionally display repeated menu titles when clicking to select group #3281
• We fixed an issue where selecting a group messed up the focus of the main table / entry editor. Focus on an entry lost when selecting a group even if the entry is within the group #3367
• We fixed an issue where composite author names were sorted incorrectly. Incorrect sorting of authors with multiple surnames in the author/editor column #2828
• We fixed an issue where the custom file column were sorted incorrectly. Sorting in columns corresponding to additional file types not working #3119
• We fixed an issues where the entry losses focus when a field is edited and at the same time used for sorting. New entry not selected in entry table when entering data in field used for sorting #3373
• We fixed an issue where the menu on Mac OS was not displayed in the usual Mac-specific way. Menu bar at wrong position on Mac OS #3146
• We fixed an issue where the groups tree of the last database was still shown even after the database was already closed.
• We fixed an issue where the "Open file dialog" may disappear behind other windows. FileChooser can go to the background #3410
• We fixed an issue where the default icon of a group was not colored correctly.
• We reworked the "Edit file" dialog to make it resizeable and improved the workflow for adding and editing files Resizing of the window "Select files" does not scale properly #2970
• We fixed an issue where the month was not shown in the preview IEEE preview does not display month #3239.

Changed:

• The special fields like Printed and Read status now show gray icons when the row is hovered.
• We added a button in the tab header which allows you to close the database with one click. Add Tab close button to tab title #494
• Sorting in the main table now takes information from cross-referenced entries into account. Year sorting does not work for crossref entries #2808
• If a group has a color specified, then entries matched by this group have a small colored bar in front of them in the main table.
• Change default icon for groups to a circle because a colored version of the old icon was hard to distinguish from its black counterpart.
• In the main table, the context menu appears now when you press the "context menu" button on the keyboard. feature request in the forum
• We added icons to the group side panel to quickly switch between union and intersection group view mode 4.0 Groups: fast access to View options #3269

Removed:

• The feature to "mark entries" was removed and merged with the groups functionality. For migration, a group is created for every value of the __markedentry field and the entry is added to this group.
• The number column was removed.
• We removed the coloring of cells in the maintable according to whether the field is optional/required.
• We removed a few commands from the right-click menu that are not needed often and thus don't need to be placed that prominently:
  • Print entry preview: available through entry preview
  • All commands related to marking: marking is not yet reimplemented
  • Set/clear/append/rename fields: available through Edit menu
  • Manage keywords: available through Edit menu
  • Copy linked files to folder: available through File menu

Migrated features:

• Sorting (Shift + click for multi-column sort)
• Filtering by search and groups
• Context menu (with linked files) for the file icon
• Right-click menu
• Setting special fields like reading status / priority / ... through the main table

I would like to ask all contributors with write-access to complete the lists above (with links to a comment with further details if necessary) with new bugs or missing features as they are discovered.

[koppor]

This should be kept

[koppor]

The left side is correct. No double "the".

[koppor]

Remove this line - is already present on line 17

[tobiasdiez]

So I now fixed the language tests as well as some other failing tests. This is now good to go as our now master branch. @koppor please be so kind and do the git magic!

@JabRef/developers please go through the issues you reported and check whether they still exists in the most recent version and if yes please create a normal issue for them (or immediately fix them).

[koppor]

Depends on #4015

(Trying out https://github.com/ahmed-taj/dep)

[koppor]

Since there are conflicts, I did the following:

1. git fetch origin --prune - to ensure I have the latest commits
2. git checkout master - to be on the master branch
3. git pull - to ensure I have the latest updates at the master branch
4. git merge origin/maintable-beta - to merge this PR
5. Open IntelliJ
6. Wait for indexing being finished
7. VCS -> Git -> Resolve conflicts
   
8. Double click each file
   
9. At each file
10. Apply all non-conflicting changes
    
11. Resolve conflicts manually

Notes of important things I did during the merge:

1. Restored ExportAction.java. (But id not wire it into the existing code. Maybe, it can be deleted?)

• Modified in the PR Fix custom exporter not displayed in file chooser #4015
• Deleted in commit de4b416

2. Kept the deletion of gui/importer/ImportFormats.java

• I think, the commits 71fcea5, 576588a, and 2f5f2e5 for ImportFormats.java have to be ported to a certain place somehow. One can do git checkout 2f5f2e5bbe2b42319736bd735791b0b3039096f6, then gitk --all src/main/java/org/jabref/gui/importer/ImportFormats.java&, then git checkout master to a) see what changed in that file and b) to continue working

3. I had to do some compile fixes:

• 55c3626
• 3044350

To create the new branch v4.x, I checkout 9b2fedc (git checkout 9b2fedc238d1ba64875c96cf8), created a new branch v4.x (git checkout -b v4.x) and made it known to our GitHub repo: git push --set-upstream origin v4.x.